Major aspects of cellular physiology are regulated by the phosphorylation state of proteins through the action of protein kinases and protein phosphatases. Phosphorylation of proteins by endogenous protein kinase activity was assayed in homogenates from guinea pig inner ear tissues with [gamma-32P] ATP. Phosphoproteins showed distinct distributions in organ of Corti, lateral wall and spiral ganglion. In the organ of Corti, several protein kinase activities were distinguished by their activation by appropriate agonists: protein kinase C, calmodulin-dependent protein kinases and cyclic nucleotide-dependent protein kinases. Twelve putative substrates for these kinases were identified in organ of Corti on the basis of increased 32P-incorporation with addition of lipids, calmodulin, and cyclic nucleotides, respectively. In addition, differences in phosphorylation were observed between the base and apex of the organ of Corti. 32P-incorporation into proteins of molecular weights between 45 and 100 kDa was significantly higher in apical tissue than in tissue from the base. In contrast, phosphate incorporation into proteins of around 29 kDa was much lower in apical tissues than in basal tissues. Furthermore, labeling of both the high and low molecular weight proteins from the apex but not the base markedly increased in response to calcium. These data indicate the presence of differential modes of regulation that may underlie structural and functional gradients along the sensory epithelium.